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Fulltext Development and validation of an instrument to assess the knowledge and perceptions of predatory journals

Marar S, Hamza MA, Ayyash M, Abu-Shaheen A

Heliyon, 2023 Nov;9(11):e22270.
PMID: 38045152 DOI: 10.1016/j.heliyon.2023.e22270

OBJECTIVE: The main aim of this study is to develop a valid and reliable instrument to assess levels of knowledge and perceptions of predatory journals.
METHODS: The current study employed successive methods framework including (1) item generation through a literature review and theoretical framework development, (2) validity testing in terms of face, content, and construct validity for perceptions construct as well as item analysis for knowledge scale, and (3) reliability testing in terms of Cronbach's alpha, Kuder-Richardson (KR-20), item-to-total correlations, corrected item-to-total correlations, Cronbach's alpha if item deleted, and test-retest reliability. A total of 304 participants were recruited from King Fahad Medical City (KFMC) in Riyadh, Saudi Arabia to evaluate its construct validity and reliability. This was established using exploratory factor analysis (EFA) with principal axis factoring (PFA) and varimax rotation as well as confirmatory factor analysis (CFA) for perception construct.
RESULTS: An instrument was developed from this study called the "Predatory Journals KP Assessment Questionnaire". The results of EFA and CFA confirmed the construct validity of the perception construct. Item analysis confirmed the construct validity of the knowledge scale. The internal consistency and test-retest reliability were achieved for the knowledge scale items, consisting of 13 items. The results of EFA confirmed the measured constructs of perceptions toward predatory journals. The results of EFA and CFA for perception construct resulted in only one factor with 9 items.
CONCLUSION: This study has successfully developed a valid and reliable questionnaire to measure knowledge and perceptions of predatory journals among researchers in the clinical and health disciplines. This instrument serves as a valuable guide for future studies that aim to assess researcher's knowledge and perceptions about predatory journals and examine the differences in these measured constructs according to their demographic and professional characteristics.
Fulltext Multivariate analysis of factors affecting presence and/or agenesis of third molar tooth

Alam MK, Hamza MA, Khafiz MA, Rahman SA, Shaari R, Hassan A

PLoS One, 2014;9(6):e101157.
PMID: 24967595 DOI: 10.1371/journal.pone.0101157

To investigate the presence and/or agenesis of third molar (M3) tooth germs in orthodontics patients in Malaysian Malay and Chinese population and evaluate the relationship between presence and/or agenesis of M3 with different skeletal malocclusion patterns and sagittal maxillomandibular jaw dimensions. Pretreatment records of 300 orthodontic patients (140 males and 160 females, 219 Malaysian Malay and 81 Chinese, average age was 16.27±4.59) were used. Third-molar agenesis was calculated with respect to race, genders, number of missing teeth, jaws, skeletal malocclusion patterns and sagittal maxillomandibular jaw dimensions. The Pearson chi-square test and ANOVA was performed to determine potential differences. Associations between various factors and M3 presence/agenesis groups were assessed using logistic regression analysis. The percentages of subjects with 1 or more M3 agenesis were 30%, 33% and 31% in the Malaysian Malay, Chinese and total population, respectively. Overall prevalence of M3 agenesis in male and female was equal (P>0.05). The frequency of the agenesis of M3s is greater in maxilla as well in the right side (P>0.05). The prevalence of M3 agenesis in those with a Class III and Class II malocclusion was relatively higher in Malaysian Malay and Malaysian Chinese population respectively. Using stepwise regression analyses, significant associations were found between Mx (P<0.05) and ANB (P<0.05) and M3 agenesis. This multivariate analysis suggested that Mx and ANB were significantly correlated with the M3 presence/agenesis.
Fulltext Computational analysis of dimer G6PD structure to elucidate pathogenicity of G6PD variants

Chandran S, Louis NE, Amran SI, Ab Latif N, Hamza MA, Alonazi M

Biomedicine (Taipei), 2024;14(1):47-59.
PMID: 38533298 DOI: 10.37796/2211-8039.1431

An inherent genetic enzyme disorder in humans, known as glucose-6-phosphate dehydrogenase (G6PD) deficiency, arises due to specific mutations. While the prevailing approach for investigating G6PD variants involves biochemical analysis, the intricate structural details remain limited, impeding a comprehensive understanding of how different G6PD variants of varying classes impact their functionality. This study 22 examined the dynamic properties of G6PD wild types and six G6PD variants from 23 different classes using molecular dynamic simulation (MDS). The wild-type and variant 24 G6PD structures unveil high fluctuations within the amino acid range of 274-515, the structural NADP+ binding site, pivotal for enzyme dimerization. Specifically, two variants, G6PDZacatecas (R257L) and G6PDDurham (K238R), demonstrate compromised structural stability at the dimer interface, attributable to the disruption of a salt bridge involving Glu 206 and Lys 407, along with the disturbance of hydrogen bonds formed by Asp 421 at the βN-βN sheets. Consequently, this impairment cascades to affect the binding affinity of crucial interactions, such as Lys 171-Glucose-6-Phosphate (G6P) and Lys 171-catalytic NADP+, leading to diminished enzyme activity. This study underscores the utility of computational in silico techniques in predicting the structural alterations and flexibility of G6PD variants. This insight holds promise for guiding future endeavors in drug development targeted at mitigating the impacts of G6PD deficiency.
Fulltext Preliminary Study of Structural Changes of Glucose-6-Phosphate Dehydrogenase Deficiency Variants

Louis NE, Hamza MA, Baharuddin PNEB, Chandran S, Latif NA, Alonazi MA, et al.

Biomedicine (Taipei), 2022;12(3):12-19.
PMID: 36381187 DOI: 10.37796/2211-8039.1355

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency disorder affecting over 400 million individuals worldwide. G6PD protects red blood cells (RBC) from the harmful effects of oxidative substances. There are more than 400 G6PD mutations, of which 186 variants have shown to be linked to G6PD deficiency by decreasing the activity or stability of the enzyme. Different variants manifest different clinical phenotypes which complicate comprehending the mechanism of the disease. In order to carry out computational approaches to elucidate the structural changes of different G6PD variants that are common to the Asian population, a complete G6PD monomer-ligand complex was constructed using AutoDock 4.2, and the molecular dynamics simulation package GROMACS 4.6.7 was used to study the protein dynamics. The G410D and V291M variants were chosen to represent classes I and II respectively and were created by in silico site-directed mutagenesis. Results from the Root mean square deviation (RMSD), Root mean square fluctuation (RMSF) and Radius of gyration (Rg) analyses provided insights on the structure - function relationship for the variants. G410D indicated impaired dimerization and structural NADP binding while the impaired catalytic activity for V291M was indicated by a conformational change at its mutation site.
A computational study of structural analysis of Class I human glucose-6-phosphate dehydrogenase (G6PD) variants: Elaborating the correlation to chronic non-spherocytic hemolytic anemia (CNSHA)

Alakbaree M, Abdulsalam AH, Ahmed HH, Ali FH, Al-Hili A, Omar MSS, et al.

Comput Biol Chem, 2023 Jun;104:107873.
PMID: 37141793 DOI: 10.1016/j.compbiolchem.2023.107873

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect that affects more than 500 million people worldwide. Individuals affected with G6PD deficiency may occasionally suffer mild-to-severe chronic hemolytic anemia. Chronic non-spherocytic hemolytic anemia (CNSHA) is a potential result of the Class I G6PD variants. This comparative computational study attempted to correct the defect in variants structure by docking the AG1 molecule to selected Class I G6PD variants [G6PDNashville (Arg393His), G6PDAlhambra (Val394Leu), and G6PDDurham (Lys238Arg)] at the dimer interface and structural NADP+ binding site. It was followed by an analysis of the enzyme conformations before and after binding to the AG1 molecule using the molecular dynamics simulation (MDS) approach, while the severity of CNSHA was determined via root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen bonds, salt bridges, radius of gyration (Rg), solvent accessible surface area analysis (SASA), and principal component analysis (PCA). The results revealed that G6PDNashville (Arg393His) and G6PDDurham (Lys238Arg) had lost the direct contact with structural NADP+ and salt bridges at Glu419 - Arg427 and Glu206 - Lys407 were disrupted in all selected variants. Furthermore, the AG1 molecule re-stabilized the enzyme structure by restoring the missing interactions. Bioinformatics approaches were also used to conduct a detailed structural analysis of the G6PD enzyme at a molecular level to understand the implications of these variants toward enzyme function. Our findings suggest that despite the lack of treatment for G6PDD to date, AG1 remains a novel molecule that promotes activation in a variety of G6PD variants.